FMO DATABASE

FMODB ID: 3979L

Calculation Name: 3JTG-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3JTG

Chain ID: A

ChEMBL ID:

UniProt ID: Q3UPW2

Base Structure: X-ray

Registration Date: 2023-06-22

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	95
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-798444.803018
FMO2-HF: Nuclear repulsion	758116.220844
FMO2-HF: Total energy	-40328.582174
FMO2-MP2: Total energy	-40447.260045

3D Structure Molmil

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:272:GLY)

Summations of interaction energy for fragment #1(A:272:GLY)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-2.661	1.45	5.467	-5.286	-4.291	-0.033

Interaction energy analysis for fragmet #1(A:272:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.052 / q_NPA : 0.028

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	274	HIS	0	-0.016	-0.006	3.789	-0.112	1.414	-0.010	-0.849	-0.666	0.002
4	A	275	LEU	0	0.005	-0.001	5.355	-0.498	-0.498	0.000	0.000	0.000	0.000
5	A	276	TRP	0	0.052	0.000	6.943	-0.142	-0.142	0.000	0.000	0.000	0.000
6	A	277	GLU	-1	-0.797	-0.884	2.358	-2.349	-0.904	5.117	-3.789	-2.773	-0.031
7	A	278	PHE	0	0.025	0.005	4.440	-0.156	-0.056	-0.001	-0.013	-0.085	0.000
8	A	279	ILE	0	-0.031	-0.026	5.725	0.290	0.290	0.000	0.000	0.000	0.000
9	A	280	ARG	1	0.812	0.870	2.483	-0.116	0.419	0.352	-0.431	-0.457	-0.003
10	A	281	ASP	-1	-0.839	-0.898	3.636	-2.586	-2.081	0.009	-0.204	-0.310	-0.001
11	A	282	ILE	0	0.001	-0.011	7.092	0.183	0.183	0.000	0.000	0.000	0.000
12	A	283	LEU	0	-0.052	-0.020	10.273	0.124	0.124	0.000	0.000	0.000	0.000
13	A	284	ILE	0	-0.034	-0.008	7.968	0.083	0.083	0.000	0.000	0.000	0.000
14	A	285	HIS	1	0.833	0.912	8.730	0.564	0.564	0.000	0.000	0.000	0.000
15	A	286	PRO	0	0.027	0.010	12.644	-0.002	-0.002	0.000	0.000	0.000	0.000
16	A	287	GLU	-1	-0.789	-0.883	13.666	-0.309	-0.309	0.000	0.000	0.000	0.000
17	A	288	LEU	0	-0.028	-0.012	11.276	0.012	0.012	0.000	0.000	0.000	0.000
18	A	289	ASN	0	-0.078	-0.030	14.346	-0.010	-0.010	0.000	0.000	0.000	0.000
19	A	290	GLU	-1	-0.781	-0.872	15.747	-0.156	-0.156	0.000	0.000	0.000	0.000
20	A	291	GLY	0	0.036	0.020	18.407	0.007	0.007	0.000	0.000	0.000	0.000
21	A	292	LEU	0	-0.029	-0.003	13.943	0.004	0.004	0.000	0.000	0.000	0.000
22	A	293	MET	0	-0.045	-0.026	11.368	0.015	0.015	0.000	0.000	0.000	0.000
23	A	294	LYS	1	0.884	0.941	16.744	0.181	0.181	0.000	0.000	0.000	0.000
24	A	295	TRP	0	0.064	0.023	12.836	0.005	0.005	0.000	0.000	0.000	0.000
25	A	296	GLU	-1	-0.873	-0.910	18.413	-0.147	-0.147	0.000	0.000	0.000	0.000
26	A	297	ASN	0	0.010	-0.023	20.396	0.012	0.012	0.000	0.000	0.000	0.000
27	A	298	ARG	1	0.880	0.954	14.426	0.230	0.230	0.000	0.000	0.000	0.000
28	A	299	HIS	0	0.087	0.054	17.986	-0.016	-0.016	0.000	0.000	0.000	0.000
29	A	300	GLU	-1	-0.915	-0.944	19.864	-0.124	-0.124	0.000	0.000	0.000	0.000
30	A	301	GLY	0	0.045	0.015	16.241	-0.004	-0.004	0.000	0.000	0.000	0.000
31	A	302	VAL	0	-0.013	-0.011	16.159	-0.028	-0.028	0.000	0.000	0.000	0.000
32	A	303	PHE	0	-0.002	-0.002	13.359	-0.007	-0.007	0.000	0.000	0.000	0.000
33	A	304	LYS	1	0.875	0.919	17.452	0.180	0.180	0.000	0.000	0.000	0.000
34	A	305	PHE	0	0.000	-0.006	14.030	-0.015	-0.015	0.000	0.000	0.000	0.000
35	A	306	LEU	0	-0.034	-0.017	18.262	0.029	0.029	0.000	0.000	0.000	0.000
36	A	307	ARG	1	0.831	0.893	19.112	0.219	0.219	0.000	0.000	0.000	0.000
37	A	308	SER	0	0.021	0.013	18.134	-0.020	-0.020	0.000	0.000	0.000	0.000
38	A	309	GLU	-1	-0.736	-0.890	17.732	-0.233	-0.233	0.000	0.000	0.000	0.000
39	A	310	ALA	0	0.012	0.024	18.536	-0.003	-0.003	0.000	0.000	0.000	0.000
40	A	311	VAL	0	0.017	0.003	12.692	-0.026	-0.026	0.000	0.000	0.000	0.000
41	A	312	ALA	0	-0.021	-0.012	13.695	-0.066	-0.066	0.000	0.000	0.000	0.000
42	A	313	GLN	0	-0.010	-0.012	15.315	-0.008	-0.008	0.000	0.000	0.000	0.000
43	A	314	LEU	0	0.032	0.027	12.173	0.004	0.004	0.000	0.000	0.000	0.000
44	A	315	TRP	0	0.003	0.000	6.876	-0.043	-0.043	0.000	0.000	0.000	0.000
45	A	316	GLY	0	0.021	-0.008	11.746	0.005	0.005	0.000	0.000	0.000	0.000
46	A	317	GLN	0	-0.015	-0.002	13.067	0.002	0.002	0.000	0.000	0.000	0.000
47	A	318	LYS	1	0.920	0.968	5.029	1.248	1.248	0.000	0.000	0.000	0.000
48	A	319	LYS	1	0.827	0.918	7.381	0.749	0.749	0.000	0.000	0.000	0.000
49	A	320	LYS	1	0.931	0.979	11.929	-0.031	-0.031	0.000	0.000	0.000	0.000
50	A	321	ASN	0	0.030	0.005	15.064	0.038	0.038	0.000	0.000	0.000	0.000
51	A	322	SER	0	0.022	0.001	17.304	-0.032	-0.032	0.000	0.000	0.000	0.000
52	A	323	ASN	0	0.031	0.033	19.560	0.010	0.010	0.000	0.000	0.000	0.000
53	A	324	MET	0	-0.075	-0.016	14.367	0.008	0.008	0.000	0.000	0.000	0.000
54	A	325	THR	0	0.054	0.020	18.340	0.008	0.008	0.000	0.000	0.000	0.000
55	A	326	TYR	0	0.007	-0.006	16.918	-0.009	-0.009	0.000	0.000	0.000	0.000
56	A	327	GLU	-1	-0.827	-0.881	18.845	-0.169	-0.169	0.000	0.000	0.000	0.000
57	A	328	LYS	1	0.916	0.956	18.421	0.148	0.148	0.000	0.000	0.000	0.000
58	A	329	LEU	0	0.012	0.020	12.828	-0.010	-0.010	0.000	0.000	0.000	0.000
59	A	330	SER	0	-0.006	-0.016	15.299	-0.012	-0.012	0.000	0.000	0.000	0.000
60	A	331	ARG	1	0.890	0.945	17.645	0.153	0.153	0.000	0.000	0.000	0.000
61	A	332	ALA	0	-0.008	0.002	13.534	0.022	0.022	0.000	0.000	0.000	0.000
62	A	333	MET	0	0.002	0.006	12.667	-0.021	-0.021	0.000	0.000	0.000	0.000
63	A	334	ARG	1	0.859	0.904	15.187	0.187	0.187	0.000	0.000	0.000	0.000
64	A	335	TYR	0	-0.004	-0.007	16.151	0.027	0.027	0.000	0.000	0.000	0.000
65	A	336	TYR	0	0.008	-0.003	9.502	-0.037	-0.037	0.000	0.000	0.000	0.000
66	A	337	TYR	0	0.041	0.030	15.285	0.021	0.021	0.000	0.000	0.000	0.000
67	A	338	LYS	1	0.936	0.975	18.664	0.085	0.085	0.000	0.000	0.000	0.000
68	A	339	ARG	1	0.943	0.967	11.127	0.160	0.160	0.000	0.000	0.000	0.000
69	A	340	GLU	-1	-0.765	-0.856	16.167	-0.078	-0.078	0.000	0.000	0.000	0.000
70	A	341	ILE	0	-0.024	0.009	10.646	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	342	LEU	0	-0.045	-0.025	12.417	-0.041	-0.041	0.000	0.000	0.000	0.000
72	A	343	GLU	-1	-0.804	-0.898	15.380	-0.110	-0.110	0.000	0.000	0.000	0.000
73	A	344	ARG	1	0.844	0.923	18.977	0.106	0.106	0.000	0.000	0.000	0.000
74	A	345	VAL	0	0.028	0.013	20.573	0.007	0.007	0.000	0.000	0.000	0.000
75	A	346	ASP	-1	-0.838	-0.934	23.200	-0.118	-0.118	0.000	0.000	0.000	0.000
76	A	347	GLY	0	0.004	0.004	26.336	0.002	0.002	0.000	0.000	0.000	0.000
77	A	348	ARG	1	0.884	0.943	24.283	0.142	0.142	0.000	0.000	0.000	0.000
78	A	349	ARG	1	0.999	0.987	23.832	0.107	0.107	0.000	0.000	0.000	0.000
79	A	350	LEU	0	-0.015	-0.010	20.508	-0.002	-0.002	0.000	0.000	0.000	0.000
80	A	351	VAL	0	-0.015	-0.001	19.585	-0.024	-0.024	0.000	0.000	0.000	0.000
81	A	352	TYR	0	-0.041	-0.028	16.230	0.005	0.005	0.000	0.000	0.000	0.000
82	A	353	LYS	1	0.917	0.951	17.131	0.141	0.141	0.000	0.000	0.000	0.000
83	A	354	PHE	0	-0.022	-0.004	9.625	-0.013	-0.013	0.000	0.000	0.000	0.000
84	A	355	GLY	0	-0.001	0.012	14.448	0.027	0.027	0.000	0.000	0.000	0.000
85	A	356	LYS	1	0.890	0.934	14.992	0.062	0.062	0.000	0.000	0.000	0.000
86	A	357	ASN	0	-0.066	-0.028	14.250	0.023	0.023	0.000	0.000	0.000	0.000
87	A	358	SER	0	-0.054	-0.039	10.576	-0.022	-0.022	0.000	0.000	0.000	0.000
88	A	359	SER	0	-0.003	-0.008	9.828	0.013	0.013	0.000	0.000	0.000	0.000
89	A	360	GLY	0	0.045	0.021	8.691	-0.066	-0.066	0.000	0.000	0.000	0.000
90	A	361	TRP	0	-0.034	-0.028	9.494	-0.085	-0.085	0.000	0.000	0.000	0.000
91	A	362	LYS	1	0.857	0.926	11.760	0.170	0.170	0.000	0.000	0.000	0.000
92	A	363	GLU	-1	-0.921	-0.988	15.188	-0.162	-0.162	0.000	0.000	0.000	0.000
93	A	364	GLU	-1	-0.921	-0.941	17.717	-0.076	-0.076	0.000	0.000	0.000	0.000
94	A	365	GLU	-1	-0.825	-0.896	12.642	-0.161	-0.161	0.000	0.000	0.000	0.000
95	A	366	VAL	0	-0.029	-0.009	11.204	-0.023	-0.023	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:272:GLY)